Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char

Abstract

Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of nonmodel organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwise F = 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in nonbreeding years. Genome scans and genetic-environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in nonmodel organisms in logistically challenging environments such as the Arctic.

Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence‐related genes

“…This haploblock overlaps a region of the genome responding to domestication selection in North America S. salar (Liu et al., ; Mäkinen et al., ) and also contains a SNP differentiating wild and domestic Norwegian S. salar (Karlsson et al., ). A homologous region was recently found to be associated with migratory difficulty (a function of distance and altitude gain) in Arctic char (Moore et al., ). Following Liu et al.…”

“…A candidate haploblock at on Ssa13, associated with freshwater migration distance, overlaps neuronal PAS domain protein 2 (npas2; (Karlsson et al, 2011). A homologous region was recently found to be associated with migratory difficulty (a function of distance and altitude gain) in Arctic char (Moore et al, 2017). Following Liu et al (2017), we hypothesize that the target of selection is a regulatory element for downstream melanocortin 4 receptor (mc4r).…”

“…This can both improve our understanding of evolutionary diversification in general and help guide management of these ecologically and culturally important taxa (e.g., Prince et al, 2017). Recent studies have identified suites of loci potentially involved with adaptation to the natal or migratory environment (e.g., Micheletti, Matala, Matala, & Narum, 2018;Moore et al, 2017), associated with ecotypic differentiation (e.g., Veale & Russello, 2017a), or responding to directional selection (e.g., Liu et al, 2017). One finding of such studies is that life-history diversification, in particular, can be underlain by single genomic regions of large effect.…”

Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Homarus americanus) as a case study

“…Individual GBS library was prepared following Mascher, Wu, and Amand (2013) and detailed in Moore et al (2017). Briefly, genomic DNA was double-digested using the PstI and MspI restriction enzymes followed by ligation to a unique barcoded adapter for each individual.…”

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

“…A total of 2,088 individuals was collected from 58 sample sites located along the Pacific coast from California to Alaska (S1 Table and Figure 1). DNA was extracted from all individuals and sequenced using a GBS method (protocol detailed in [97]). Reads were aligned to the Coho salmon reference genome v1 (GCF_002021745.1) using bwa-mem 0.7.13 [102].…”